update to add provisional module files.

These just contain logger set up. Actual documentation and impolementations are required.

phasecalculator/analysis/fgipanalysis.py

+# -*- coding: utf-8 -*-
+#    phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+#    Copyright (C) 2019  Mark D. Driver
+#
+#    phasecalculator is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU Affero General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU Affero General Public License for more details.
+#
+#    You should have received a copy of the GNU Affero General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+"""
+Created on Tue Jan  7 16:34:17 2020
+
+@author: Mark
+"""
+
+import logging
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+

phasecalculator/analysis/similarityanalysis.py

+# -*- coding: utf-8 -*-
+#    phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+#    Copyright (C) 2019  Mark D. Driver
+#
+#    phasecalculator is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU Affero General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU Affero General Public License for more details.
+#
+#    You should have received a copy of the GNU Affero General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+"""
+Created on Tue Jan  7 16:34:17 2020
+
+@author: Mark
+"""
+
+import logging
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+

phasecalculator/analysis/vleanalysis.py

+# -*- coding: utf-8 -*-
+#    phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+#    Copyright (C) 2019  Mark D. Driver
+#
+#    phasecalculator is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU Affero General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU Affero General Public License for more details.
+#
+#    You should have received a copy of the GNU Affero General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+"""
+Created on Tue Jan  7 16:34:17 2020
+
+@author: Mark
+"""
+
+import logging
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+

phasecalculator/io/phasecalculatorxmlparser.py

+# -*- coding: utf-8 -*-
+#    phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+#    Copyright (C) 2019  Mark D. Driver
+#
+#    phasecalculator is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU Affero General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU Affero General Public License for more details.
+#
+#    You should have received a copy of the GNU Affero General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+"""
+Created on Tue Jan  7 16:34:17 2020
+
+@author: Mark
+"""
+
+import logging
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+

phasecalculator/io/polynomialio.py

+# -*- coding: utf-8 -*-
+#    phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+#    Copyright (C) 2019  Mark D. Driver
+#
+#    phasecalculator is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU Affero General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU Affero General Public License for more details.
+#
+#    You should have received a copy of the GNU Affero General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+"""
+Created on Tue Jan  7 16:34:17 2020
+
+@author: Mark
+"""
+
+import logging
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+

phasecalculator/phasecalculatorcli.py

+# -*- coding: utf-8 -*-
+#    phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+#    Copyright (C) 2019  Mark D. Driver
+#
+#    phasecalculator is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU Affero General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU Affero General Public License for more details.
+#
+#    You should have received a copy of the GNU Affero General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+"""
+Created on Tue Jan  7 16:34:17 2020
+
+@author: Mark
+"""
+
+import logging
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+

phasecalculator/runners/fgipanalysisrunner.py

+# -*- coding: utf-8 -*-
+#    phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+#    Copyright (C) 2019  Mark D. Driver
+#
+#    phasecalculator is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU Affero General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU Affero General Public License for more details.
+#
+#    You should have received a copy of the GNU Affero General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+"""
+Created on Tue Jan  7 16:34:17 2020
+
+@author: Mark
+"""
+
+import logging
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+

phasecalculator/runners/phasetransferrunner.py

+# -*- coding: utf-8 -*-
+#    phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+#    Copyright (C) 2019  Mark D. Driver
+#
+#    phasecalculator is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU Affero General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU Affero General Public License for more details.
+#
+#    You should have received a copy of the GNU Affero General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+"""
+Created on Tue Jan  7 16:34:17 2020
+
+@author: Mark
+"""
+
+import logging
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+

phasecalculator/runners/similarityanalysisrunner.py

+# -*- coding: utf-8 -*-
+#    phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+#    Copyright (C) 2019  Mark D. Driver
+#
+#    phasecalculator is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU Affero General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU Affero General Public License for more details.
+#
+#    You should have received a copy of the GNU Affero General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+"""
+Created on Tue Jan  7 16:34:17 2020
+
+@author: Mark
+"""
+
+import logging
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+

phasecalculator/test/analysistest/fgipanalysistest.py

+# -*- coding: utf-8 -*-
+#    phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+#    Copyright (C) 2019  Mark D. Driver
+#
+#    phasecalculator is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU Affero General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU Affero General Public License for more details.
+#
+#    You should have received a copy of the GNU Affero General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+"""
+Created on Tue Jan  7 16:34:17 2020
+
+@author: Mark
+"""
+
+import logging
+import unittest
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+

phasecalculator/test/phasecalculatortests.py

+# -*- coding: utf-8 -*-
+#    phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+#    Copyright (C) 2019  Mark D. Driver
+#
+#    phasecalculator is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU Affero General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU Affero General Public License for more details.
+#
+#    You should have received a copy of the GNU Affero General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+"""
+Created on Tue Jan  7 16:34:17 2020
+
+@author: Mark
+"""
+
+import logging
+import unittest
+import sys
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+IO_TEST_CASES = []
+
+RUNNERS_TEST_CASES = []
+
+ANALYSIS_TEST_CASES = []
+
+MODULE_TEST_CASES = []
+
+def create_test_suite():
+    """Create a test suite with all the tests from the package.
+
+    Returns
+    -------
+    suite : test suite
+        test suite with all tests of package loaded.
+
+    """
+    LOGGER.info("setting up loader and test suite")
+    loader = unittest.TestLoader()
+    suite = unittest.TestSuite()
+    for test_case in IO_TEST_CASES:
+        LOGGER.debug("Adding %s", test_case)
+        suite.addTests(loader.loadTestsFromTestCase(test_case))
+    for test_case in RUNNERS_TEST_CASES:
+        LOGGER.debug("Adding %s", test_case)
+        suite.addTests(loader.loadTestsFromTestCase(test_case))
+    for test_case in ANALYSIS_TEST_CASES:
+        LOGGER.debug("Adding %s", test_case)
+        suite.addTests(loader.loadTestsFromTestCase(test_case))
+    for test_case in MODULE_TEST_CASES:
+        LOGGER.debug("Adding %s", test_case)
+        suite.addTests(loader.loadTestsFromTestCase(test_case))
+    return suite
+
+
+def run_tests():
+    """Run test suite. Exits if there is a failure.
+
+    Returns
+    -------
+    None
+    """
+    LOGGER.info("calling test suite method")
+    suite = create_test_suite()
+    LOGGER.info("running test suite")
+    ret = (
+        not unittest.TextTestRunner(verbosity=2, stream=sys.stderr)
+        .run(suite)
+        .wasSuccessful()
+    )
+    if ret:
+        sys.exit(ret)
+
+
+if __name__ == "__main__":
+    run_tests()